It would be much easier if you use mount points.
For example- mount the second hard disk, assuming with a single partition, as /recs.
If you need date directories for your recordings then set the FTP script to move them there, by setting ftp home directory in /recs/whatever. You may want to try a modified script, which deletes files when ftp-ing them:
http://www.vicidial.org/VICIDIALmantis/view.php?id=197
If you don't need date directories, then just point AST_CRON_audio_2_compress.pl to a symlink in the newly created /recs directory. In this case the FTP script becomes obsolete.
Getting the idea?
Modification of /etc/astguiclient.conf and apache.conf if you are using alias to access recordings may also be needed. Just giving you a rough idea to think on.